I marked this post as a question and added tags to increase visibility.
Would you mind elaborating on where exactly in the software you are trying to set these peak annotations? Are you right-clicking in the signal window and selecting Properties>Annotations? Or are you editing the properties of a report item on a report template? If it is the latter, what type of report template are you using (Intelligent Report, Advanced Report, or Standard Report)?
If you are right-clicking in the signal window and selecting Properties>Annotations, how many places are the decimal are you selecting to display for Width at 50% height?
If you have very sharp, narrow peaks then you might need to increase the number of places after the decimal to a value greater than the default value of 2.
I actually solved this. I just wanted EZChrom to measure the width at 50 % height. Upon selecting Width at 50 % height in the trace annotation properties, it labelled the peaks with 0.00 as the width. When I went back to Analyze the single chromatogram, it calculated the peak at 50 % height like I had wanted and annotated it with the width.